def assess_alignment(alignment: pysam.AlignedSegment, alignment_info: Dict):
""" Compare alignment against reference alignment"""
chrom_match = alignment.reference_name == alignment_info['chrom']
# assess reference bases that match between the two reads
matching_pos = np.array(alignment.get_reference_positions(full_length=False))
base_range = (matching_pos >= alignment_info['start']) & (matching_pos <= alignment_info['end'])
matching_prop = sum(base_range) / len(alignment_info['cigar'])
return chrom_match, matching_prop
referenceid = str(reference) + ' '
refnucpos1 = 0 + (3 * refcodonpos)
refnucpos2 = 1 + (3 * refcodonpos)
refnucpos3 = 2 + (3 * refcodonpos)
if 1 <= (refcodonpos + 1) <= 9:
refcodonposid = str(refcodonpos + 1) + " "
else:
refcodonposid = str(refcodonpos + 1)
refAAid = str(Seq(codon).translate()[0])
# loop over all reads to find AAs
marker_list = []
for read in samfile.fetch():
read_codon = []
#loop through base and its pos at the same time
for seq, pos in zip(read.seq,
AlignedSegment.get_reference_positions(read)):
if pos == refnucpos1:
read_codon.append(seq)
if pos == refnucpos2:
read_codon.append(seq)
if pos == refnucpos3:
read_codon.append(seq)
if any(read_codon) is True:
if len(read_codon) == 3:
counter += 1
if ''.join(read_codon) == codon:
marker_list.append('.')
else:
marker_list.append(
str(Seq("".join(read_codon)).translate()[0]))
print(referenceid, refcodonposid, refAAid, counter,
def __call__(self):
fastaFile = pysam.FastaFile(self.args.fastainput)
bamFile = pysam.AlignmentFile(self.args.BAMinput, "rb")
ssl_settings = {'ca':self.args.sslpath}
con = MySQLdb.connect(self.args.server, self.args.user, self.args.password, self.args.database, ssl=ssl_settings)
with con:
cur = con.cursor()
cur.execute("USE " + self.args.database)
def batch_gen(data, batch_size):
for i in range(0, len(data), batch_size):
yield data[i:i+batch_size]
references = sorted(set(bamFile.getrname(read.tid) for read in samfile.fetch()))
referencesLeng = sorted(set(len(fastaFile.fetch(reference=str(item)))for item in references))
for ref, leng in zip(references, referencesLeng):
print ref, leng
cur.execute('INSERT INTO templates(protein, length) VALUES(%s, %s)' ,(ref, leng))
for reference in references:
returned_position_lines=[]
length=0
refcodonpos=0
counter=0
for codon in batch_gen(fastaFile.fetch(reference=str(reference)),3):
length+=3
markerlist=[]
referenceid = str(reference)+ ' '
refnucpos1=0 +(3*refcodonpos)
refnucpos2=1 +(3*refcodonpos)
refnucpos3=2 +(3*refcodonpos)
if 1 <= (refcodonpos+1) <= 9:
refcodonposid = str(refcodonpos+1)+ " "
else:
refcodonposid = str(refcodonpos+1)
refAAid = str(Seq(codon).translate()[0])
marker_list=[]
for read in samfile.fetch():
read_codon=[]
for seq, pos in zip(read.seq,AlignedSegment.get_reference_positions(read)):
if pos == refnucpos1:
read_codon.append(seq)
if pos == refnucpos2:
read_codon.append(seq)
if pos == refnucpos3:
read_codon.append(seq)
if any(read_codon) is True:
if len(read_codon) == 3:
counter+=1
if ''.join(read_codon) == codon:
marker_list.append('.')
else:
marker_list.append(str(Seq("".join(read_codon)).translate()[0]))
print (referenceid, refcodonposid, refAAid, counter, ''.join(str(item)for item in marker_list))
returned_position_lines.append(''.join(str(item)for item in marker_list))
cur.execute("INSERT INTO sites(template_id, position, wild_type_AA) VALUES((SELECT id from templates WHERE protein=%s), %s, %s)" ,(reference, refcodonposid, refAAid))
counter=0
refcodonpos+=1
print returned_position_lines
AAs = ('A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P','S','T','W','Y','V','*')
for AA in AAs:
position=0
for line in returned_position_lines:
position+=1
count=0
for readAA in line:
if readAA==AA:
count+=1
if (count >= 1):
print count, AA, position
cur.execute("INSERT INTO substitutions(site_id, substitution, count) VALUES((SELECT id from sites WHERE position=%s AND template_id=(SELECT id from templates WHERE protein=%s)), %s, %s)" ,(position, reference, AA, count))
con.commit()
fastaFile.close()
bamFile.close()
